Variant report

Variant	rs8078723
Chromosome Location	chr17:38166879-38166880
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:38166854-38166917	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:38165802..38167535-chr17:38239576..38241169,2	K562	blood:

Variant related genes	Relation type
CSF3	TF binding region
ENSG00000126351	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1042658	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1045929	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.97[LWK][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11078934	0.84[CEU][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap];0.87[EUR][1000 genomes]
rs11655264	0.92[YRI][hapmap]
rs11658328	0.85[YRI][hapmap]
rs11871747	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12600856	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12602172	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12941811	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2227315	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2227322	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2227336	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2241245	0.85[YRI][hapmap]
rs2305482	0.87[MKK][hapmap];0.85[YRI][hapmap]
rs3213762	0.86[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3826331	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3859192	0.88[MKK][hapmap]
rs3935280	0.83[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs4065321	0.90[MKK][hapmap];0.85[YRI][hapmap]
rs4794822	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4794823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4794824	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4795412	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4795414	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4795415	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4795416	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4795418	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4795419	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4795420	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55771023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55846942	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56922390	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57065891	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57968500	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59925331	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60082402	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62065177	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6503530	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7021	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs709591	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs709592	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7208815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7209755	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7214085	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7221894	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7222039	0.98[ASN][1000 genomes]
rs7502514	0.84[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs7502912	0.84[CHD][hapmap]
rs8065443	0.83[CHB][hapmap]
rs8065519	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8066582	0.90[MKK][hapmap];0.85[YRI][hapmap]
rs8067817	0.98[ASN][1000 genomes]
rs8068260	0.91[ASN][1000 genomes]
rs8070454	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8072548	0.98[ASN][1000 genomes]
rs8073254	0.84[YRI][hapmap]
rs8075668	0.90[MKK][hapmap];0.89[YRI][hapmap]
rs8081692	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs868150	0.83[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap]
rs9303283	0.82[CHB][hapmap];0.85[YRI][hapmap]
rs9915252	0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492308	chr17:38033039-38204458	Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv908220	chr17:38153473-38175426	Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
White blood cell count	21738480	GWAS catalog
C-reactive protein and white blood cell count	22788528	GWAS catalog

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs8078723	GSDMA	cis	Artery Aorta	GTEx
rs8078723	PSMD3	cis	Lymphoblastoid	GTEx
rs8078723	MED24	cis	Nerve Tibial	GTEx
rs8078723	PCGF2	cis	cerebellum	SCAN
rs8078723	GSDMA	cis	Adipose Subcutaneous	GTEx
rs8078723	PSMD3	cis	multi-tissue	Pritchard
rs8078723	GSDMA	cis	lung	GTEx
rs8078723	GSDMB	cis	cerebellum	SCAN
rs8078723	PSMD3	cis	Frontal Cortex	GTEx
rs8078723	PSMD3	cis	parietal	SCAN
rs8078723	MED24	cis	cerebellum	SCAN
rs8078723	MED24	cis	Artery Tibial	GTEx
rs8078723	GSDMA	cis	Esophagus Muscularis	GTEx
rs8078723	MED24	cis	Artery Aorta	GTEx
rs8078723	MED24	cis	parietal	SCAN
rs8078723	MED24	cis	Thyroid	GTEx
rs8078723	GSDMA	cis	Nerve Tibial	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38153800-38172200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr17:38154600-38170000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr17:38154600-38170200	Weak transcription	Esophagus	oesophagus
4	chr17:38154800-38173600	Weak transcription	Thymus	Thymus
5	chr17:38155000-38170000	Weak transcription	HSMM	muscle
6	chr17:38155000-38173600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr17:38155000-38174000	Weak transcription	Fetal Brain Female	brain
8	chr17:38155400-38170200	Weak transcription	Placenta	Placenta
9	chr17:38155600-38169600	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr17:38155600-38169800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr17:38155800-38171800	Weak transcription	Spleen	Spleen
12	chr17:38164600-38171600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr17:38165200-38169800	Weak transcription	K562	blood
14	chr17:38166400-38167000	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr17:38166600-38167000	Enhancers	NHEK	skin
16	chr17:38166600-38168000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr17:38166800-38169000	Weak transcription	Fetal Thymus	thymus
18	chr17:38166800-38169600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr17:38166800-38169600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr17:38166800-38169600	Weak transcription	Stomach Mucosa	stomach
21	chr17:38166800-38169800	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr17:38166800-38169800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr17:38166800-38169800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr17:38166800-38169800	Weak transcription	Fetal Lung	lung
25	chr17:38166800-38169800	Weak transcription	Dnd41	blood
26	chr17:38166800-38170000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr17:38166800-38173400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr17:38166800-38173800	Weak transcription	Primary T cells from cord blood	blood
29	chr17:38166800-38174600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr17:38166800-38177400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr17:38166800-38178200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr17:38166800-38181600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links